Quantifying heterogeneity and dynamics of clonal fitness in response to perturbation

Journal of Cellular Physiology

Volumn 230, Issue 7, 2015, Pages 1403-1412

  Frick, Peter L ^a   Paudel, Bishal B ^a   Tyson, Darren R ^a   Quaranta, Vito ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4 (4 FLUOROPHENYL) 2 (4 METHYLSULFINYLPHENYL) 5 (4 PYRIDYL)IMIDAZOLE; ANISOMYCIN; CYCLOHEXIMIDE; TRAMETINIB; PROTEIN SYNTHESIS INHIBITOR;

ARTICLE; CELL CLONE; CELL CLONING; CELL COUNT; CELL CULTURE; CELL HETEROGENEITY; CELL MOTILITY; CELL POPULATION; CELL PROLIFERATION; CELL PROLIFERATION ASSAY; CLONAL FITNESS; CLONAL FRACTIONAL PROLIFERATION; CLONAL VARIATION; CONTROLLED STUDY; GROWTH INHIBITION; IMMUNOHISTOCHEMISTRY; PERTURBATION INDUCED PROLIFERATION; PRIORITY JOURNAL; CELL LINE; CULTURE TECHNIQUE; DRUG EFFECTS; GENE EXPRESSION REGULATION; GENETICS; HUMAN; PHYSIOLOGY; REPRODUCTIVE FITNESS;

MAMMALIA;

CELL CULTURE TECHNIQUES; CELL LINE; CELL PROLIFERATION; CLONE CELLS; CYCLOHEXIMIDE; GENE EXPRESSION REGULATION; GENETIC FITNESS; HUMANS; PROTEIN SYNTHESIS INHIBITORS;

EID: 84925652325     PISSN: 00219541     EISSN: 10974652     Source Type: Journal    
DOI: 10.1002/jcp.24888     Document Type: Article

References (29)

1. Anaka M, Hudson C, Lo P-H, Do H, Caballero OL, Davis ID, Dobrovic A, Cebon J, Behren A. 2013. Intratumoral genetic heterogeneity in metastatic melanoma is accompanied by variation in malignant behaviors. BMC Med Genomics 6:40.
2. Anderson AR, Weaver AM, Cummings PT, Quaranta V. 2006. Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell 127:905-915.
3. Azzalini A. 2005. The skew-normal distribution and related multivariate families. Scand J Stat 32:159-188.
4. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S. 2004. Bacterial persistence as a phenotypic switch. Science 305:1622-1625.
5. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jane'-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. 2012. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483:603-607.
6. Brock A, Chang H, Huang S. 2009. Non-genetic heterogeneity-a mutation-independent driving force for the somatic evolution of tumours. Nature Rev Genet 10:336-342.
7. Chin TM, Quinlan MP, Singh A, Sequist LV, Lynch TJ, Haber DA, Sharma SV, Settleman J. 2008. Reduced Erlotinib sensitivity of epidermal growth factor receptor-mutant non-small cell lung cancer following cisplatin exposure: A cell culture model of second-line erlotinib treatment. Clin Cancer Res 14:6867-6876.
8. Dexter DL, Kowalski HM, Blazar BA, Fligiel Z, Vogel R, Heppner GH. 1978. Heterogeneity of tumor cells from a single mouse mammary tumor. Cancer Res 38:3174-3181.
9. Ferreiro I, Joaquin M, Islam A, Gomez-Lopez G, Barragan M, Lombardía L, Domínguez O, Pisano DG, Lopez-Bigas N, Nebreda AR, Posas F. 2010. Whole genome analysis of p38 SAPK-mediated gene expression upon stress. BMC Genomics 11:144.
10. Georgescu W, Wikswo JP, Quaranta V. 2012. CellAnimation: An open source MATLAB framework for microscopy assays. Bioinformatics 28:138-139.
11. Gilmartin AG, Bleam MR, Groy A, Moss KG. 2011. GSK1120212 (JTP-74057) is an inhibitor of MEK activity and activation with favorable pharmacokinetic properties for sustained in vivo pathway inhibition. Clin Cancer Res 17:989-1000.
12. Gordo I, Perfeito L, Sousa A. 2012. Fitness effects of mutations in bacteria. J Mol Microbiol Biotechnol 21:20-35.
13. Gordo I, Campos PRA. 2013. Evolution of clonal populations approaching a fitness peak. Biol Lett 9:20120239.
14. Hipfner DR, Cohen SM. 2004. Connecting proliferation and apoptosis in development and disease. Nat Rev Mol Cell Biol 5:805-815.
15. Huang S. 2009. Non-genetic heterogeneity of cells in development: More than just noise. Development 136:3853-3862.
16. Kreso A, Kreso A, O'Brien CA, van Galen P, Gan OI, Notta F, Brown AM, Ng K, Ma J, Wienholds E, Dunant C, Pollett A, Gallinger S, McPherson J, Mullighan CG, Shibata D, Dick JE. 2013. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science 339:543-548.
17. Kuczek T, Axelrod DE. 1987. Tumor cell heterogeneity: Divided-colony assay for measuring drug response. Proc Natl Acad Sci USA 84:4490-4494.
18. Liu X, Yang J-M, Zhang SS, Liu X-Y, Liu DX. 2010. Induction of cell cycle arrest at G1 and S phases and cAMP-dependent differentiation in C6 glioma by low concentration of cycloheximide. BMC Cancer 10:684.
19. Michor F, Hughes TP, Iwasa Y, Branford S, Shah NP, Sawyers CL, Nowak MA. 2005. Dynamics of chronic myeloid leukaemia. Nature 435:1267-1270.
20. Nowell PC. 1976. The clonal evolution of tumor cell populations. Science 194:23-28.
21. Porter SN, Baker LC, Mittelman D, Porteus MH. 2014. Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo. Genome Biol 15:R75.
22. Rasband WS. 2008. ImageJ (http://rsbweb.nih.gov/ij/).
23. Rooswinkel RW, van de Kooij B, Verheij M, Borst J. 2012. Bcl-2 is a better ABT-737 target than Bcl-xL or Bcl-w and only Noxa overcomes resistance mediated by Mcl-1, Bfl-1, or Bcl-B. Cell Death Dis 3:e366.
24. Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A. 2008. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132:487-498.
25. Shaul YD, Seger R. 2007. The MEK/ERK cascade: From signaling specificity to diverse functions. Biochimica Et Biophysica Acta (BBA)-Mol Cell Res 1773:1213-1226.
26. Sporn MB, Harris ED. 1981. Proliferative diseases. Am J Med 70:1231-1236.
27. Tsai J, Lee JT, Wang W, Zhang J, Cho H, Mamo S, Bremer R, Gillette S, Kong J, Haass NK, Sproesser K, Li L, Smalley KSM, Fong D, Zhu Y, Marimuthu A, Nguyen H, Lam B, Liu J, Cheung I, Rice J, Suzuki Y, Luu C, Settachatgul C, Shellooe R, Cantwell J, Kim S, Schlessinger J, Zhang KYJ, West BL, Powell B, Habets G, Zhang C, Ibrahim PN, Hirth P, Artis DR, Herlyn M, Bollag G. 2008. Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity. Proc Natl Acad Sci 105:3041-3046.
28. Tyson DR, Garbett SP, Frick PL, Quaranta V. 2012. Fractional proliferation: A method to deconvolve cell population dynamics from single-cell data. Nat Methods 9:923-928.
29. Zuleta IA, Aranda-Díaz A, Li H, El-Samad H. 2014. Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods 11:443-448.